Identification of protein associations
The three human proteins ACE2, TMPRSS2 and FURIN used by SARS-CoV-2 to efficiently entry into human cells were studied for their functional protein associations using the STRING database. TMPRSS2 was networked as a center point associated with both ACE2 and FURIN, while ACE2 and FURIN showed no interactions between each other (Supplementary Figure 1). In order to study the immune system interactions of the human targets, the GO term immune system process’ (GO: 0002376) from the Gene Ontology resource was analyzed. In total, 2811 genes (Supplementary Table 1) were studied for functional protein association networks using STRING (string-db.org). This analysis produced 24072 protein associations (Supplementary Table 2), among which ACE2 shared 21 protein associations (Figure 1A), while TMPRSS2 shared 17 protein associations (Figure 1B). With 64 proteins, FURIN indicated the highest associations (Figure 1C). Among the protein associations within the three HT-SARS-CoV-2, DPP4 shared associations with ACE2, TMPRSS2 and FURIN (Figure 2), while ADAM17, glycoprotein 2 (GP2), transferrin receptor 1 (TFGC) were the common network elements with ACE2 and FURIN. CTSL, GAPDH, MYC, AKT1 and SRC were functionally associated with TMPRSS2 and FURIN (Table 1).
Although no genes were co-expressed at significant levels (p ≤ 0.05) (Table 1), DPP4 was co-expressed with the three HT-SARS-CoV-2 analyzed with a p-value of 0.06. Likewise, FURIN with ADAM17 (p 0.063) and MYC (p 0.061) and CTSL with TMPRSS2 (p 0.061) and FURIN (p 0.062) shared coexpression patterns. The top text-mining score was obtained by FURIN/GP2 (0.859) followed by ACE2/DPP4 (0.717) and ACE2/ADAM17 (0.706). On the other hand, ACE2/DPP4 had the highest STRING score (0.942) followed by FURIN/GP2 and (0.859) and ACE2/ADAM17 (0.707) (Table 1).
Determination of genes correlating with HT-SARS-CoV-2 in cancer
The ACE2, TMPRSS2 and FURIN expression was correlated to every single gene in the five different datasets described in Materials and Methods. The top ~ 1500 genes of the respective association i.e., having a highly significant correlation (p < 0.01) in the corresponding dataset, are summarized in Supplementary Table 3. From the common STRING associations between our human target genes, 19 associations of 8 commonly networking genes were plotted to the 3 HT-SARS-CoV-2 (Table 2) in mixed healthy (323 samples) and cancer (11003 samples) tissues. Such collected data allowed a classification in four distinct segments: (i) associations between human target genes, (ii) triple association of DPP4 and (iii) double associations of FURIN with either ACE2 or (iv) with TMPRSS2, respectively. The top segment of Table 2 represents the positive correlations involving TMPRSS2 in both healthy and tumor datasets. The central association marker, DPP4 positively correlates with ACE2 (normal: R 0.308; cancers: 0.382), TMPRSS2 (normal: R 0.524; cancers: 0.382) and FURIN (normal: R 0.498; cancers: R 0.246) in both datasets (Figure 3). ADAM17 exhibits negative correlations with ACE2 (normal: R -0.187; cancers: R - 0.044) and FURIN (normal: R -0.281; cancers: R -0.079). GP2 and TFRC showed differential association patterns with ACE2 and FURIN. The common TMPRSS2 and FURIN associated genes, CTSL, MYC, AKT1 and SRC, displayed positive correlations with their corresponding subjects except for FURIN and MYC correlation in cancers (R 0.012; p 0.199). TMPRSS2 negatively correlated with GAPDH (Table 2).
To explore gene association patterns in the wide range of datasets, ACE2, TMPRSS2 and FURIN were correlated to DPP4, SRC and ADAM17 expression regardless of the tissue and the disease. ACE2 and TMPRSS2 displayed a positive correlation, whereas FURIN showed a negative correlation with their counterparts (Table 3 and Figure 3).
Correlation pattern of SARS-CoV-2 targets in pancreatic tissues
Healthy pancreatic tissues exhibit distinct associations when compared to pancreatic cancer tissues or tissue samples from patients suffering from diabetes mellitus. The HT-SARS-CoV2 ACE2 and TMPRSS2 were positively associated with healthy pancreatic tissue, while a non-significant positive association was noted in the context of cancer and diabetes mellitus. A positive correlation between TMPRSS2 and FURIN was found in the diseased, but not in the healthy pancreas (Table 3). Interestingly, ACE2 and DPP4 were connected irrespective of the pancreatic nature. DPP4 was differentially expressed with TMPRSS2 and FURIN; TMPRSS2 was positively expressed in healthy and negatively expressed in the diseased pancreas.
FURIN expression was not correlated with DPP4 except for pancreatic cancer, where a negative correlation was found. The FURIN/ADAM17 axis remained negatively associated with pancreatic tissues. Interestingly, TMPRSS2 positively correlated with SRC in the pancreatic tissues in mixed healthy and cancer datasets. Other double associating genes lack any specific correlation pattern. FURIN and MYC were positively associated with healthy tissues and pancreatic cancer. However, FURIN acted positively with MYC in pancreatic cancer, but not in the mixed cancer dataset. AKT1 with TMPRSS2 and FURIN were positively correlated in all contexts except for pancreatic cancer and healthy pancreas, respectively. Interestingly, many networking genes were not correlated in pancreatic tissues. These include ACE2/ADAM17, FURIN/GAPDH, ACE2/FURIN, ACE2/GP2 and ACE2/TFRC, respectively.
Identification of drug candidates for HT-SARS-CoV-2 and co-expressed genes
A total of 16 target drugs (Table 4) and 32 drug-associated genes (Supplementary Table 4) were acquired from STITCH analysis. As shown in Figure 3, ACE2/DPP4 and FURIN/ADAM17 were predicted to have drug connections, whereas TMPRSS2/SRC had no predicted drug connection. Several inhibitors of the angiotensin receptor (ACE) and DPP4, such as sitagliptin, teneligliptin, linagliptin, vildagliptin and saxagliptin, were identified. For FURIN and ADAM17 therapeutic involvement via calcium ions and Zn (II and in addition for ADAM17, an involvement via IK-682 were identified.