Pan-cancer analysis combined with experiments predicts CTHRC1 as a therapeutic target for human cancers

Abstract

Background: The function of collagen triple helix repeat containing 1 (CTHRC1) as an oncogene has been reported in a growing number of publications. Bioinformatics methods represent a beneficial approach to examine the mechanism and function of the CTHRC1 gene in the disease process of cancers from a pan-cancer perspective.

Methods: In this study, using the online databases UCSC, NCBI, HPA, TIMER2, Oncomine, GEPIA, UALCAN, cBioPortal, COSMIC, MEXPRESS, STRING, CCLE, LinkedOmics, GTEx, TCGA, CGGA, and SangerBox, we focused on the relationship between CTHRC1 and tumorigenesis, progression, methylation, immunity, and prognosis. qPCR was used to detect CTHRC1 expression in glioma tissues and cell lines.

Results: The pan-cancer analysis showed that CTHRC1 was overexpressed in most tumors, and a significant correlation was observed between CTHRC1 expression and the prognosis of patients with cancer. CTHRC1 genetic alterations occur in diverse tumors and are associated with tumor progression. Levels of CTHRC1 promoter methylation were decreased in most cancer tissues compared with normal tissues. In addition, CTHRC1 coordinated the activity of ICP genes through diverse signal transduction pathways, was also associated with immune cell infiltration and the tumor microenvironment, and potentially represented a promising immunotherapy target. We identified CTHRC1-related genes across cancers using the GEPIA2 tool. The single-gene GO analysis of CTHRC1 across cancers showed that it was involved in some signaling pathways and biological processes, such as the Wnt signaling pathway, cell migration, and positive regulation of protein binding. The expression and function of CTHRC1 were also further verified in glioma tissues and cell lines.

Conclusions: CTHRC1 is overexpressed in various cancer types and functions as an important oncogene that may promote tumorigenesis and development through different mechanisms. CTHRC1 may represent an important therapeutic target for human cancers.

Keywords: CTHRC1; Expression; Immune; Methylation; Pan-cancer; Prognosis.

Fig. 1

CTHRC1 characteristics and its expression levels in normal tissues and cancers. a Genomic location of human CTHRC1 gene; b CTHRC1 consensus Normalized eXpression (NX) levels for 55 normal tissue types and 6 blood cell types, created by combining the data from the three transcriptomics datasets (HPA, GTEx and FANTOM5); c Increased or decreased CTHRC1 mRNA in data sets of different cancers compared with normal tissues in the Oncomine database; d Human CTHRC1 mRNA expression levels in different tumor types from TCGA database were determined by TIMER; e The differences in expression levels of CTHRC1 mRNA in different tumors and normal tissues from TCGA and GTEx database were determined by SangerBox; (*P < 0.05, ** P < 0.01, *** P < 0.001)

Fig. 2

CTHRC1 protein expression, conservation and location. a CTHRC1 protein expression data in 44 normal tissues; b Conservation of CTHRC1 protein among different species; c The phylogenetic tree of CTHRC1 in different species; d CTHRC1 protein is sited in the nucleus of RH-30 cell, DAPI for the nucleus in blue, the CTHRC1 protein staining is shown in green; e CTHRC1 protein can be secreted (red circle); f The percentage of cancer patients (maximum 12 patients) with high and medium protein expression level

Fig. 3

Correlation between CTHRC1 mRNA expression and prognosis of cancers. a We used the GEPIA2 tool to perform overall survival and disease-free survival analyses of pan-cancer in TCGA by CTHRC1 mRNA expression; b The relationships between CTHRC1 expression and OS prognosis of different cancers in “Gene-KM plotter” module of SangerBox. The Kaplan–Meier plotter was performed survival analyses, including OS, DMFS, RFS, PPS, FP DSS, via the expression level of the CTHRC1 mRNA in breast cancer, liver cancer and lung cancer cases c, and OS, PFS, PPS, FP, via the expression level of the CTHRC1 mRNA in ovarian cancer and gastric cancer (d)

Fig. 4

Mutation feature of CTHRC1 in different tumors. Mutation features of CTHRC1 for tumors was analyzed using the cBioPortal tool. The alteration frequency with mutation type a and mutation site b are displayed. The potential correlation between mutation status and disease-specific was also analyzed c, progression-free d, overall e and disease-free f survival of all TCGA tumors using the cBioPortal tool

Fig. 5

Methylation level of CTHRC1 DNA in different tumors and its association with gene expression. a–c Promoter methylation levels of CTHRC1 in different cancer types compared to normal adjacent tissues. The Beta value indicates level of DNA methylation ranging from 0 (unmethylated) to 1 (fully methylated). Different beta value cut-off has been considered to indicate hyper-methylation [Beta value: 0.7—0.5] or hypo-methylation [Beta-value: 0.3—0.25]. d The relationship between the CTHRC1 mRNA expression (RNA-seq or Affy) and DNA methylation in glioma in CCLE database. e We used the MEXPRESS approach to analyze the DNA methylation level of CTHRC1 with multiple probes. The promoter region probes are highlighted by red rectangle. The beta value of methylation, the Benjamini-Hochberg-adjusted P-value and the Pearson correlation coefficients (R) are displayed

Fig. 6

CTHRC1 expression and immune infiltration. a Correlation of CTHRC1 expression with immune infiltration level in LIHC, COAD, and CESC; b Different algorithms were used to explore the potential correlation between the expression level of CTHRC1 gene and the infiltration level of CD8 + T cells across all types of cancer in TCGA; c TIMER algorithm was used to explore the potential correlation between the expression level of CTHRC1 gene and the infiltration level of CD8 + T cells in LGG and GBM

Fig. 7

CTHRC1-related gene enrichment analysis. a CTHRC1-binding proteins obtained by using the STRING tool; b The corresponding heatmap data in the detailed cancer types are displayed. The partial correlation (cor) and P-value was generated via the purity-adjusted Spearman's rank correlation test; c Using the GEPIA2 approach, we also obtained the top 10 CTHRC1-correlated genes in TCGA projects and analyzed the expression correlation between CTHRC1 and selected targeting genes

Fig. 8

The expression of CTHRC1 in glioma tissues and cell lines. a, b CTHRC1 mRNA expression levels were detected in 43 glioma cases. c Expression of CTHRC1 was determined in human astrocyte and GBM cell lines