Increased TRIM31 gene expression is positively correlated with SARS-CoV-2 associated genes TMPRSS2 and TMPRSS4 in gastrointestinal cancers

Abstract

Besides typical respiratory symptoms, COVID-19 patients also have gastrointestinal symptoms. Studies focusing on the gastrointestinal tumors derived from gastrointestinal tissues have raised a question whether these tumors might express higher levels of SARS-CoV-2 associated genes and therefore patients diagnosed with GI cancers may be more susceptible to the infection. In this study, we have analyzed the expression of SARS-CoV-2 associated genes and their co-expressions in gastrointestinal solid tumors, cancer cell lines and patient-derived organoids relative to their normal counterparts. Moreover, we have found increased co-expression of TMPRSS2-TMPRSS4 in gastrointestinal cancers suggesting that SARS-CoV-2 viral infection known to be mediated by this protease pair might facilitate the effects of viral infection in GI cancer patients. Further, our findings also demonstrate that TRIM31 expression is upregulated in gastrointestinal tumors, while the inhibition of TRIM31 significantly altered viral replication and viral processes associated with cellular pathways in gastrointestinal cancer samples. Taken together, these findings indicate that in addition to the co-expression of TMPRSS2-TMPRSS4 protease pair in GI cancers, TRIM31 expression is positively correlated with this pair and TRIM31 may play a role in providing an increased susceptibility in GI cancer patients to be infected with SARS-CoV-2 virus.

Figure 1

Heatmap of RNA-sequencing-based gene expression from the SARS-CoV-2-associated genes generated using GTEx portal for a multi-gene query in seven gastrointestinal tissues. (a) Comparison of the genes in different gastrointestinal normal samples. (b) TCGA tumor-normal samples and GTEx samples together (T tumor, N normal, TPM Transcripts per kilobase million-expresses RNA-sequencing reads normalized for the length of gene and sequencing depth).

Figure 2

Correlation analysis results of TMPRSS2 and TMPRSS4 genes in gastrointestinal cancer tissues. Relationship of TMPRSS2 and TMPRSS4 with respect to their expression values shows moderate positive correlation (R-value > 0.3) in COAD, READ, ESCA and PAAD (a–d) and weak positive correlation in STAD samples (e).

Figure 3

Positive correlation between TMPRSS2 and TMPRSS4 in gastrointestinal cancer cell lines from CCLE database. For colorectal (a), stomach (b) and pancreatic (c) cancer cell lines, R-value > 0.5 and for esophagus cancer cell lines (d) R-value > 0.3 while p-values for all of them < 0.05.

Figure 4

Cancer type-wise expression of eight genes (a; SH3BGRL2, b; TJP3, c; TRIM31) in TCGA gastrointestinal solid tumor samples. Red boxes are tumor samples while gray ones are normal and boxplots with ‘*’ sign shows statistically significant differential gene expression value, p-value < 0.05. Gene Expression Profiling Interactive Analysis: colon adenocarcinoma (COAD), rectal adenocarcinoma (READ), esophagus adenocarcinoma (ESCA), pancreas adenocarcinoma (PAAD), stomach adenocarcinoma (STAD).

Figure 5

Correlation analysis of the TMPRRS2, TMPRSS4 and TRIM31 genes across patient derived organoids. Positive correlation between TMPRSS2&TMPRSS4 and TRIM31 was observed in colorectal cancer organoids (n = 87) (a,b). Only TMPRSS2 shows a significant positive correlation with TMPRSS4 (n = 17) but no significant correlation is observed between the serin protease pair and TRIM31 in pancreatic cancer organoids (c,d).

Figure 6

PPI network analysis for affected genes when TRIM31 was silenced in 20 CRC cell lines using rnai. while upregulated genes with red circles exhibited weak co-expression score (less than 0.5), blue circles indicating downregulated genes showed co-expression score bigger than 0.5 (a). Blue circles exhibiting downregulated genes are highlighted with red coloured text exhibited 18 nodes indicating similar processes using gene ontology analysis (b). The 18 nodes indicating cellular processes that mostly affected by TRIM31 silencing are presented by the names of these proteins and their cellular function such as viral transcription & viral processes, RNA binding, and ribosome small subunit biogenesis are listed (c). Majority of these cellular processes that are affected by TRIM31 silencing in crc cell lines are related to viral transcription & viral processes.