Gene expression analysis of heat-shock proteins and redox regulators reveals combinatorial prognostic markers in carcinomas of the gastrointestinal tract

Abstract

Heat shock proteins (HSPs) are a large family of ubiquitously expressed proteins with diverse functions, including protein assembly and folding/unfolding. These proteins have been associated with the progression of various gastrointestinal tumours. Dysregulation of cellular redox has also been associated with gastrointestinal carcinogenesis, however, a link between HSPs and dysregulation of cellular redox in carcinogenesis remains unclear. In this study, we analysed mRNA co-expression and methylation patterns, as well as performed survival analysis and gene set enrichment analysis, on gastrointestinal cancer data sets (oesophageal, stomach and colorectal carcinomas) to determine whether HSP activity and cellular redox dysregulation are linked. A widespread relationship between HSPs and cellular redox was identified, with specific combinatorial co-expression patterns demonstrated to significantly alter patient survival outcomes. This comprehensive analysis provides the foundation for future studies aimed at deciphering the mechanisms of cooperativity between HSPs and redox regulatory enzymes, which may be a target for future therapeutic intervention for gastrointestinal tumours.

Keywords: Gastrointestinal carcinomas; Gene expression analysis; Heat shock proteins (HSPs); Redox regulators.

Graphical abstract

Fig. 1

Co-expression analysis of HSPs and redox regulators in gastrointestinal tumours. Heatmaps of Spearman's rank correlation coefficient (ρ) for all HSP and redox genes (A, C,E) and selected gene combinations (B, D,F) in the following TCGA datasets: colorectal carcinoma (A, B), stomach adenocarcinoma (C, D), oesophageal carcinoma (E, F). In all panels, blue indicates negative ρ, red indicates positive ρ. In panels B, D and F, circle size indicates magnitude of ρ.

Fig. 2

Single gene survival analysis of HSPs and redox regulators in oesophageal carcinoma. A) Heatmap of log-rank p-values for overall survival differences of HSPs and redox regulators in oesophageal carcinoma. Blue indicates significant (p < 0.05) survival differences, Red indicates non-significant (p > 0.05) survival differences. Overall survival analysis for B) HSPD1^high vs HSPD1^low C) DNAJA1^high vs DNAJA1^low D) SEC63^high vs SEC63^low. E) Heatmap of log-rank p-values for disease-free survival differences of HSPs and redox regulators in oesophageal carcinoma. Overall disease-free survival analysis for F) PRDX2^high vs PRDX2^low G) CCT4^high vs CCT4^low H) DNAJB5^high vs DNAJB5^low I) GPX4^high vs GPX4^low.

Fig. 3

Single gene survival analysis of HSPs and redox regulators in stomach adenocarcinoma. A) Heatmap of log-rank p-values for overall survival differences of HSPs and redox regulators in stomach adenocarcinoma. Blue indicates significant (p < 0.05) survival differences, Red indicates non-significant (p > 0.05) survival differences. Overall survival analysis for B) CCT8^high vs CCT8^low C) DNAJC19^high vs DNAJAC19^low D) GAK^high vs GAK^low E) SEC63^high vs SEC63^low. F) Heatmap of log-rank p-values for disease-free survival differences of HSPs and redox regulators in stomach adenocarcinoma. Disease-free survival analysis for G) DNAJA4^high vs DNAJA4^low H) DNAJC13^high vs DNAJC13^low I) HSPA4^high vs HSPA4^low

Fig. 4

Single gene survival analysis of HSPs and redox regulators in colorectal carcinoma. A) Heatmap of log-rank p-values for overall survival differences of HSPs and redox regulators in colorectal carcinoma. B) Heatmap of log-rank p-values for disease-free survival differences of HSPs and redox regulators in colorectal carcinoma. Blue indicates significant (p < 0.05) survival differences, Red indicates non-significant (p > 0.05) survival differences. C) Disease-free survival analysis for CCT2^high vs CCT2^low.

Fig. 5

Combinatorial gene survival analysis of HSPs and redox regulators in gastrointestinal cancers. Disease-free survival analysis for A) CCT4/CCT7^high vs CCT4/CCT7^low, B) CCT5/GPX1^high vs CCT5/GPX1^low C) DNAJC7/GPX1^high vs DNAJC7/GPX1^low in oesophageal carcinoma dataset. Overall survival analysis for D) HSPA9/PRDX1^high vs HSPA9/PRDX1^low E) DNAJA2/TXN^high vs DNAJA2/TXN^low and F) DNAJA2/PRDX6^high vs DNAJA2/PRDX6^low in stomach adenocarcinoma dataset. Disease-free survival analysis for G) CCT2^high/GSS^high vs CCT2^low/GSS^low H) DNAJB12^high/GSS^high vs DNAJB12^low/GSS^low I) DNAJC8^high/GSS^high vs DNAJC8^low/GSS^low in colorectal carcinoma dataset.

Fig. 6

Correlation of methylation and gene expression of HSPs and redox regulators in gastrointestinal cancers. Heatmap of Spearman's rank correlation coefficient (ρ) for TCGA datasets of A) oesophageal carcinoma B) stomach adenocarcinoma and C) colorectal carcinoma for various tumour stages (T1-T4b). Blue indicates negative Spearman's coefficient, Red indicates positive Spearman's coefficient. Green line indicates redox regulator genes, yellow line indicates HSP genes. D) Line graph plotting gene methylation to mRNA expression through tumour stages T1-T3 of HSPB9, CCT6A, GPX4 and DNAJC18 for oesophageal carcinoma dataset. E) Line graph plotting gene methylation to mRNA expression through tumour stages T1-T4b of TRAP1, DNAJC19, CCT8, DNAJA4 and GAK for stomach adenocarcinoma dataset. F) Line graph plotting gene methylation to mRNA expression through tumour stages T1-T4b of DNAJC8, and GSTM1 for colorectal carcinoma dataset.

Fig. 7

Gene set enrichment analysis (GSEA) of HSPs and redox regulators in gastrointestinal cancers. Bar graphs of normalised enrichment scores (NES) from GSEA of various HSP^high vs HSP^low phenotypes in A) colorectal carcinoma B) oesophageal adenocarcinoma and C) stomach adenocarcinoma for validation of HSP related processes. Bar graphs of normalised enrichment scores (NES) from GSEA of various redox regulators^high/low/HSP^high/low vs redox regulators^high/low/HSP^low/high phenotypes in D) colorectal carcinoma E) oesophageal carcinoma and F) stomach adenocarcinoma. Heat shock protein genes indicated by yellow writing, redox regulators indicated by green writing.

Fig. S4

A) Disease-free survival analysis for DNAJC18^high vs DNAJC18^low patients in the esophageal carcinoma dataset. B) Overall survival analysis for CCT6A^high vs CCT6A^low patients in the oesophageal carcinoma dataset.