Gene expression profiles of primary colorectal carcinomas, liver metastases, and carcinomatoses

Abstract

Background: Despite the fact that metastases are the leading cause of colorectal cancer deaths, little is known about the underlying molecular changes in these advanced disease stages. Few have studied the overall gene expression levels in metastases from colorectal carcinomas, and so far, none has investigated the peritoneal carcinomatoses by use of DNA microarrays. Therefore, the aim of the present study is to investigate and compare the gene expression patterns of primary carcinomas (n = 18), liver metastases (n = 4), and carcinomatoses (n = 4), relative to normal samples from the large bowel.

Results: Transcriptome profiles of colorectal cancer metastases independent of tumor site, as well as separate profiles associated with primary carcinomas, liver metastases, or peritoneal carcinomatoses, were assessed by use of Bayesian statistics. Gains of chromosome arm 5p are common in peritoneal carcinomatoses and several candidate genes (including PTGER4, SKP2, and ZNF622) mapping to this region were overexpressed in the tumors. Expression signatures stratified on TP53 mutation status were identified across all tumors regardless of stage. Furthermore, the gene expression levels for the in vivo tumors were compared with an in vitro model consisting of cell lines representing all three tumor stages established from one patient.

Conclusion: By statistical analysis of gene expression data from primary colorectal carcinomas, liver metastases, and carcinomatoses, we are able to identify genetic patterns associated with the different stages of tumorigenesis.

Figure 1

Dendrogram from differentially expressed genes between metastases and primary tumors. Dendrogram from hierarchical clustering of the 89 most statistical differentially expressed genes between metastases (n = 8; carcinomatoses and liver metastases together indicated in red) and primary carcinomas (n = 18 indicated in black), with a more than two-fold change derived from BAMarray.

Figure 2

Cluster analysis of differentially expressed genes between primary carcinomas, liver metastases and carcinomatoses. A) PCA of the 53 most statistical differentially expressed genes between of primary carcinomas (n = 18, black), liver metastases (n = 4, blue), and carcinomatoses (n = 4, pink) expressed over three-fold derived from BAMarray. B) HCA of the same genes, with the same color coding. Genes are colored based on association to tumor site.

Figure 3

ELAC1 downregulation in metastases. We used real-time RT-PCR to validate the expression of five genes with altered expression in metastases. ELAC1 was validated as a downregulated gene in colorectal cancer, with a particular downregulation in the liver metastases and carcinomatoses. Values are here normalized according to values from normal colon mucosa before log2-transformation. Red and blue colored circles denote results from individual samples using real time RT-PCR and microarray experiments, respectively. N, normal colon mucosa; P, primary carcinoma; L, liver metastasis; C, carcinomatosis.

Figure 4

Genome and transcriptome profiles of cell line model. A) Genomic changes in three cell lines IS1, IS2, and IS3 from a primary carcinoma, its corresponding liver- and peritoneal metastases derived from the same patient. B) Genes expressed in fold change above 2.0 in the same cell lines. 609 genes are found in common between the three cell lines, whereas 263 genes are shared between IS1 and IS2, 130 genes in common between IS1 and IS3, and 225 genes are shared between the metastases cell lines, IS2 and IS3. 551- (IS1), 406- (IS2), and 484 genes (IS3) are only seen in one cell line.