Example Studies

29 May 2020

Footprint of SARS-CoV-2

© NEBION AG. Last update: May 29, 2020

Research on developing therapeutic strategies against the SARS-CoV-2 virus currently has highest priority in many research facilities around the world. This blog regularly posts novel findings from our scientists as well as information about datasets that we have curated.

To better understand the pathobiology of COVID-19, we use GENEVESTIGATOR® (300,000+ transcriptomic datasets) to visualize the expression and regulation of various human genes involved in host infection by SARS-CoV-2. Our transcriptomic compendium representing thousands of different experimental conditions is used to identify the most relevant tissues, cell types, diseases, drugs and other conditions linked to the regulation of these genes.

UPDATE: This example study is continued in our blog, with regular updates on this topic. Go to blog

29 May 2020

Expression of priming protease Furin

SARS-Cov-2 differs from closely related coronaviruses (including SARS-Cov) in the sequence of its spike protein, among other things. Unlike SARS-Cov, the newly emerged coronavirus SARS-Cov-2 spike protein contains a multibasic furin-like S1/S2 cleavage site. A recent study has identified that cleavage of the spike protein at this site is required for SARS-CoV-2 virus entry into human lung cells (Hoffmann et al., 2020). Variation around the envelope protein cleavage site plays an important role in tissue tropism and pathogenicity of several viruses (Braun and Sauter, 2019). For instance, highly pathogenic influenza A viruses harbour a multibasic furin cleavage site, while their low pathogenic counterparts do not. In GENEVESTIGATOR®, one can easily explore the tissue expression profile of the priming protease furin (PCSK3), or other furin-like proteases. Using the 2-gene plot tool, we have shown a rather uniform expression of furin across tissues and cell types (Figure 5). Interestingly, this broad expression profile is in line with the observed broad tissue tropism of the newly emerged virus, as detected in COVID-19 patient autopsy tissue samples (Puelles et al., 2020).

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Figure 6: GENEVESTIGATOR® 2-Gene scatterplot showing the expression levels of the priming protease furin plotted against the receptor ACE2 in 13351 samples from healthy tissue and primary cells (Affymetrix Human 133 Plus2 compendium). The priming protease furin shows a ubiquitous expression in all tissue and cell types examined.

As mentioned above, the enzymatic activity of furin is known to be exploited by numerous viral and bacterial pathogens, including HIV and highly pathogenic strains of influenza. Several proteins expressed by infected cells have been shown to suppress this furin-mediated processing of viral proteins (Braun and Sauter, 2019). We have explored the regulation of three of them, GBP2, GBP5 and PAR1/F2R in response to drug/compound treatment. Among the top-20 compounds up-regulating GBP2 and GBP5 proteins, we observed several Toll-like receptor agonists such as poly I:C or LPS. Surprisingly, we also found that decitabine, a nucleic acid synthesis inhibitor, up-regulates expression of all the three antiviral proteins studied. It is tempting to speculate that dependency on host priming proteases is one of the key determinants of tissue tropism and spread of the newly emerged SARS-Cov-2 virus. They may thus represent potential targets for therapeutic intervention. Their expression and regulation certainly warrant further investigation.

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Figure 5: Top-10 compounds up-regulating the expression of guanylate‐binding protein 2 (GBP2), a protein known to inhibit furin‐mediated viral protein processing. Effects of compound treatment was investigated in 6171 samples of tissues and primary cells (Affymetrix Human 133 Plus2 compendium).

11 May 2020

Expression regulation of LY6E

Recently, Pfaender et al. (2020) reported that the lymphocyte antigen 6 complex, locus E (LY6E) protein potently restricts cellular infection by multiple coronaviruses, including SARS-CoV-2. Using GENEVESTIGATOR® across multiple compendia and platforms, we screened thousands of experimental conditions to study the gene expression regulation of LY6E. Here are some of the most significant effects we found:

Condition Description Fold-change
IFNb-1a (Avonex) HS-01577 / Neutrophils isolated from peripheral blood samples of patients with multiple sclerosis 24 hours after the first treatment with IFNb-1A (Avonex). Control: patients before treatment. 137x upregulation
Influenza HS-03257 / Plasmacytoid dendritic cells isolated from the blood of healthy donors were treated 24h with influenza A/PR/8/34 (H1N1) virus. Control: Plasmacytoid dendritic cells isolated from healthy donors. 20x upregulation
Lupus LY6E is strongly upregulated in several SLE case-control studies 10-40x upregulation
IFM-a2b HS-00230 / Immature dendritic cells treated with 1000 u/ml of IFN-a2b. Control: without treatment 7x upregulation
Brefeldin A HS-01936 / LY6E is downregulated in response to Brefeldin A treatment. 6x downregulation
Sepsis HS-01577 / LY6E is strongly downregulated in neutrophils isolated from peripheral blood samples of patients with sepsis as compared to healthy subjects. 200x downregulation

Table 1: Conditions causing an up- or downregulation of the LY6E gene, as identified using the Perturbations tool in GENEVESTIGATOR®.

30 April 2020

Conditions regulating ACE2 expression

Under the hypothesis that the expression level of the ACE2 receptor correlates with the degree of infection by the virus, we screened over 10,000 experimental conditions to identify those causing a strong up- or down-regulation of ACE2. As an example, the top up-regulating condition from the Affymetrix Human 133 Plus 2 compendium (5,738 conditions tested) is the exposure of bronchial epithelial cells to polyinosinic-polycytdidylic acid (see experimental details provided). This compound, which is structurally similar to double-stranded RNA, is a known immunostimulant used to simulate viral infections (especially RNA viruses such as SARS-CoV-2) by interacting with TLR3. This raises the question as to whether the SARS-CoV-2 virus is able to trigger the up-regulation of the ACE2 receptor, thereby increasing its own ability to infect human cells .

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Figure 4: GENEVESTIGATOR® Perturbations plot showing a subset of conditions in which ACE2 is strongly up-regulated, with a detailed view on study HS-01166 showing its reponse to poly(I:C) in bronchial epithelial cells.

9 April 2020

Tissue expression of ACE2 and TMPRSS2

To infect human cells, the SARS-CoV-2 receptor requires the presence of at least the ACE2 receptor (angiotensin-converting enzyme 2) and of the priming protease TMPRSS2 (transmembrane serine protease 2). Cell types in which both exhibit high expression are expected to be more strongly infected. The below figures, generated with GENEVESTIGATOR® were based on two large compendia of deeply curated RNA-Seq and microarray datasets. Only samples from healthy, untreated individuals were selected to visualize baseline tissue and cell type specific expression.

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Figure 3: GENEVESTIGATOR® 2-Gene scatterplot showing the expression levels of ACE2 versus TMPRSS2 in 8397 samples from 310 different tissue and cell types (Affymetrix Human 133 Plus2 compendium). The two genes show highest expression in the small intestine, the kidney, the eye, the large intestine, followed by respiratory tract tissues. Similar results were observed based on the RNA-sequencing data compendium.

Top 30 human tissues and cell-types with highest ACE2 expression

Data selected: mRNASeq samples from adult, healthy untreated subjects

post thumb Figure 2: GENEVESTIGATOR® Anatomy plot showing ACE2 expression in the top 30 of 445 tissues and cell types tested.

Top 30 human tissues and cell-types with highest TMPRSS2 expression

Data selected: mRNASeq samples from adult, healthy untreated subjects

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Figure 1: GENEVESTIGATOR® Anatomy plot showing TMPRSS2 expression in the top 30 of 445 tissues and cell types tested.

An extended visualization of ACE2 and TMPRSS2 across all 445 tissues and cell types is shown here: