Patient and tumor characteristics and correlations with ACE2 expression
A total of 38,628 tumors specimens, representing 36 tumors types, that underwent comprehensive molecular profiling at Caris Life Sciences between 2019 and 2020 were retrospectively reviewed. Molecular profiles of adjacent normal (non-cancerous) tissue from 127 tumor specimens, representing 24 tumor types, were reviewed as a control. Key demographic characteristics of these cohorts are shown in Table. Average ACE2 expression was significantly increased in patients under 65 years compared to patients 65 years and older (5.8 vs 4.8 TPM, p<0.0001), and male patients exhibited significantly higher average ACE2 expression compared to female patients (6.1 vs 4.8 TPM, p<0.0001). Pathway analysis shows that ACE2 is the most enriched gene in the renin-angiotension pathway in male gender and underexpressed in patients older than 55 years (Supplementary Figure 1, 2)
ACE2 expression across tumor types
Among the 36 tumor types investigated, median ACE2 expression was increased in 9 tumor types compared to normal tissue (0.99 TPM), with the highest ACE2 expression observed in colorectal (7.08 TPM) and kidney (5.35 TPM) cancers (Figure 1). In addition to colorectal cancer, ACE2 expression in other gastrointestinal (GI) cancers, including small intestinal (2.62 TPM), gastric (2.04 TPM), cholangiocarcinoma (1.92 TPM), esophageal/esophagogastric junction (1.29 TPM), and pancreatic (1.11 TPM) cancers, was increased relative to normal tissue. While non-small cell lung cancer (NSCLC) exhibited slightly decreased median ACE2 expression (0.95 TPM) compared to normal tissue, a subset of NSCLC tumors (N=64, 0.85%) demonstrated severely increased expression (>50 TPM). The lowest ACE2 expression was observed in melanoma (0.19 TPM), mesothelioma (0.18 TPM), and meningioma (0.16 TPM).
Protease gene expression across tumor types
Entry of SARS-CoV-2 into human cells is facilitated by priming of the viral spike protein by cellular proteases (Hoffman et al., 2020). While inhibition of the serine protease TMPRSS2 blocks SARS-CoV-2 infection of lung cells (Hoffman et al., 2020), other proteases, including cathepsin B and L (CTSB/CTSL) and FURIN, mediate spike protein priming and have cumulative effects with TMPRSS2 on viral entry (Shang et al. 2020). Median TMPRSS2 expression was increased in 16 tumor types, including NSCLC (10.35 TPM), compared to normal tissue (3.82 TPM), most notably in prostate cancer (265.43 TPM) (Figure 2). Similar to ACE2 expression, increased TMPRSS2 expression was observed in many GI cancers (colorectal: 44.02 TPM, gastric: 40.12 TPM, small intestinal: 35.69 TPM, esophageal/esophagogastric junction: 31.16 TPM, pancreatic: 17.96 TPM, cholangiocarcinoma: 14.75 TPM, liver: 9.55 TPM, and anal: 6.78 TPM). CTSB, CTSL, and FURIN expression was increased in most tumor types relative to normal tissue. CTSB expression was highest in thyroid cancer (1287.97 TPM; normal: 166.61 TPM), CTSL expression was highest in gastrointestinal stromal tumors (376.26 TPM; normal: 30.36 TPM), and FURIN expression was highest in liver cancer (55.37 TPM; normal: 16.89 TPM).
Co-expression of ACE2 and key protease genes across tumor types
We examined the co-expression of ACE2 with key protease genes to evaluate the correlation between ACE2 and protease gene expression (Figure 3). In normal tissue, the correlation with ACE2 expression was strongest for TMPRSS2 (Pearson’s correlation [r]=0.44, slope [m]=0.95) compared to CSTB (r=0.09, m=0.09), CSTL (r=-0.10, m=0.05), and FURIN (r=-0.04, m=0.14). Interestingly, most tumor types exhibited weaker ACE2/TMPRSS2 and ACE2/CTSB correlations compared to normal tissue, whereas the ACE2/CTSL and ACE2/FURIN correlations in normal tissue are weaker than that of most cancer types ([include Supplementary table of correlation coefficients]). Tumor type-specific deviations from the primary ACE2/TMPRSS2 cluster were observed for prostate (r=-0.05, m=0.06) and GI cancers (r=0.27, m=0.35), while expression in NSCLC tumors (r=0.07, m=0.46) largely overlapped with the primary cluster. Tumor type-specific deviations in ACE2/protease co-expression were less prominent for CTSB, CTSL, and FURIN compared to TMPRSS. Notably, ACE2/protease co-expression in GI cancers deviated from the primary cluster due to increased ACE2 expression (CTSB: r=-0.02, m=-0.0001; CTSL: r=-0.04, m=-0.02; FURIN: r=0.03, m=0.02). Together, this suggests the co-expression of ACE2 and protease genes may be more predictive of susceptibility to viral infection by SARS-CoV-2 than ACE2 expression alone, with GI cancers exhibiting the highest potential susceptibility.
ACE2 expression and association with cell population abundance in the TME in NSCLC
In addition to its function as a receptor for SARS-CoV-2, ACE2 is suggested to be involved in various aspects of post-infection processes, and the expression of ACE2 in lung has been shown to associate with innate and acquired immune responses23. We used the Microenvironment Cell Populations (MCP)-counter24 to estimate cell population abundance in the TME, inferred by RNA expression tested by WTS in NSCLC tumors of adenocarcinoma histology. Consistent with the previous observation of ACE2 expression level correlating with neutrophils, NK cells and various Th cells in SARS-CoV infected cells23, we observed in NSCLC tumor tissues significant positive correlations of ACE2 expression with T cells, NK cells, B cells, monocytic lineage, dendritic cells, neutrophils, as well as endothelial cells (p<0.0001), Figure 4.