Pan‑cancer analysis of transmembrane protease serine 2 and cathepsin L that mediate cellular SARS‑CoV‑2 infection leading to COVID-19

Abstract

Severe acute respiratory syndrome (SARS) coronavirus‑2 (SARS‑CoV2) is the cause of a new disease (COVID‑19) which has evolved into a pandemic during the first half of 2020. Older age, male sex and certain underlying diseases, including cancer, appear to significantly increase the risk for severe COVID‑19. SARS‑CoV‑2 infection of host cells is facilitated by the angiotensin‑converting enzyme 2 (ACE‑2), and by transmembrane protease serine 2 (TMPRSS2) and other host cell proteases such as cathepsin L (CTSL). With the exception of ACE‑2, a systematic analysis of these two other SARS‑CoV2 infection mediators in malignancies is lacking. Here, we analysed genetic alteration, RNA expression, and DNA methylation of TMPRSS2 and CTSL across a wide spectrum of tumors and controls. TMPRSS2 was overexpressed in cervical squamous cell carcinoma and endocervical adenocarcinoma, colon adenocarcinoma, prostate adenocarcinoma (PRAD), rectum adenocarcinoma (READ), uterine corpus endometrial carcinoma and uterine carcinosarcoma, with PRAD and READ exhibiting the highest expression of all cancers. CTSL was upregulated in lymphoid neoplasm diffuse large B‑cell lymphoma, oesophageal carcinoma, glioblastoma multiforme, head and neck squamous cell carcinoma, lower grade glioma, pancreatic adenocarcinoma, skin cutaneous melanoma, stomach adenocarcinoma, and thymoma. Hypo‑methylation of both genes was evident in most cases where they have been highly upregulated. We have expanded on our observations by including data relating to mutations and copy number alterations at pan‑cancer level. The novel hypotheses that are stemming out of these data need to be further investigated and validated in large clinical studies.

Keywords: cathepsin L (CTSL); transmembrane protease serine 2 (TMPRSS2); pan-cancer; DNA methylation; COVID-19; angiotensin-converting enzyme 2.

Figure 1

SARS-CoV2 attaches to the ACE-2 receptor and it can be taken into the host cell in endosomes where it can be cleaved and activated by CTSL proteases. Moreover, TMPRSS2 is co-expressed with ACE-2 on the cell membrane and it can prime the spike viral proteins, thus activating the fusion of the virus with the membrane lipid layer and facilitating the uptake into the host cell. ACE-2, angiotensin-converting enzyme 2; CTSL, cathepsin L; TMPRSS2, transmembrane protease serine 2.

Figure 2

RNA expression aberration of CTSL in tumors. (A) the gene expression profile across all tumor samples and paired normal tissues, each dot represents expression of samples. (B) The gene expression profile across all tumor samples and paired normal tissues. The height of bar represents the median expression of certain tumor type or normal tissue. CTSL, cathepsin L.

Figure 3

RNA expression aberration of TMPRSS2 in tumors. (A) the gene expression profile across all tumor samples and paired normal tissues, each dot represents expression of samples. (B) The gene expression profile across all tumor samples and paired normal tissues. The height of bar represents the median expression of certain tumor type or normal tissue. TMPRSS2, transmembrane protease serine 2.

Figure 4

Correlation of CTSL expression with methylation status. COAD and READ had lower expression in tumors (A, red) due to higher methylation status (B, red). The opposite happens on STAD with the lower methylation, to allow higher CTSL expression. In LHIC there was no significant difference in normal to tumor expression even if the methylation is higher in the cancer samples (P=1.47e-07). CTSL, cathepsin L; COAD, colon adenocarcinoma; READ, rectum adenocarcinoma; STAD, stomach adenocarcinoma; LHIC, liver hepatocellular carcinoma.

Figure 5

Correlation of TMPRSS2 expression with methylation status. PRAD and READ had higher expression in tumors (A, red) due to lower methylation status (B, red). The opposite happens on BRCA and LUSC with the higher methylation, to decrease the expression of TMPRSS2 in tumors. TMPRSS2, trans-membrane protease serine 2; PRAD, prostate adenocarcinoma; READ, rectum adenocarcinoma; BRCA, breast invasive carcinoma; LUSC, lung squamous cell carcinoma.

Figure 6

CTSL RNA expression in tissues. Consensus transcript expression levels for each gene were summarized in 74 human tissues based on transcriptomics data from three sources: HPA, GTEx and FANTOM5. The consensus NX value for each gene and organ/tissue represents the maximum NX value in the three data sources Color-coding is based on tissue groups, each consisting of tissues with functional features in common. The data include 10,953 patients/10,967 samples in 32 cancer datasets. CTSL, cathepsin L; HPA, Human Protein Atlas; GTEx, Genotype-Tissue Expression; FANTOM5, the Functional Annotation of Mammalian Genomes 5; NX, normalized expression.

Figure 7

TMPRSS2 RNA expression in tissues. Consensus transcript expression levels for each gene were summarized in 74 human tissues based on transcriptomics data from three sources: HPA, GTEx and FANTOM5. The consensus normalized expression (NX) value for each gene and organ/tissue represents the maximum NX value in the three data sources. Color-coding is based on tissue groups, each consisting of tissues with functional features in common The data include 10,953 patients/10,967 samples in 32 studies. HPA, Human Protein Atlas; GTEx, Genotype-Tissue Expression; FANTOM5, the Functional Annotation of Mammalian Genomes 5; NX, normalized expression.

Figure 8

(A) CTSL mutations were distributed across the CTSL gene (cBioPortal) with 8 hot spot mutation sites in TCGA cohort using cBioPortal and 3d hotspots (12). Mutation diagram circles are colored with respect to the corresponding mutation types. In case of different mutation types at a single position, color of the circle is determined with respect to the most frequent mutation type. Mutation types and corresponding color codes are as follows: green: Missense Mutations; black: Truncating Mutations. (B) The relevance of genetic disorders and CTSL expression where it is shown that mutations were not relevant to RNA expression. (C) DNA copy variation were not statistically relevant to RNA CTSL expression. CTSL, cathepsin L; TCGA, The Cancer Genome Atlas.

Figure 9

(A) TMPRSS2 mutations were distributed across the TMPRSS2 gene (cBioPortal) (12). Mutation diagram circles are colored with respect to the corresponding mutation types. In case of different mutation types at a single position, color of the circle is determined with respect to the most frequent mutation type. Mutation types and corresponding color codes are as follows: green: Missense mutations; black: Truncating mutations. (B) The relevance of genetic disorders and TMPRSS2 expression were as shown, in prostate cancer there is a 30% fusion of the gene and in the stomach adenocarcinoma 8% deep deletion. (C) DNA copy variation were not statistically relevant to RNA TMPRSS2 expression and as shown, many pancreatic cancer patients had deep deletions. CTSL, cathepsin L; TMPRSS2, transmembrane protease serine 2.