Microarray analysis reveals distinct gene expression profiles among different tumor histology, stage and disease outcomes in endometrial adenocarcinoma

Abstract

Background: Endometrial cancer is the most common gynecologic malignancy in developed countries and little is known about the underlying mechanism of stage and disease outcomes. The goal of this study was to identify differentially expressed genes (DEG) between late vs. early stage endometrioid adenocarcinoma (EAC) and uterine serous carcinoma (USC), as well as between disease outcomes in each of the two histological subtypes.

Methodology/principal finding: Gene expression profiles of 20 cancer samples were analyzed (EAC = 10, USC = 10) using the human genome wide illumina bead microarrays. There was little overlap in the DEG sets between late vs. early stages in EAC and USC, and there was an insignificant overlap in DEG sets between good and poor prognosis in EAC and USC. Remarkably, there was no overlap between the stage-derived DEGs and the prognosis-derived DEGs for each of the two histological subtypes. Further functional annotation of differentially expressed genes showed that the composition of enriched function terms were different among different DEG sets. Gene expression differences for selected genes of various stages and outcomes were confirmed by qRT-PCR with a high validation rate.

Conclusion: This data, although preliminary, suggests that there might be involvement of distinct groups of genes in tumor progression (late vs. early stage) in each of the EAC and USC. It also suggests that these genes are different from those involved in tumor outcome (good vs. poor prognosis). These involved genes, once clinically verified, may be important for predicting tumor progression and tumor outcome.

Figure 1. Hierarchical clustering of patient samples based on differentially expressed genes (P<0.01) obtained from comparing late stage versus early stage in the USC group and EAC group, respectively.

A) USC group. B) EAC group. In clustering dendrogram, blue stands for early stage samples while yellow stands for late stage samples. Red means up-regulated while green means down regulated.

Figure 2. Hierarchical clustering of patient samples based on differentially expressed genes (P<0.01) obtained from comparing good prognosis versus poor prognosis in the USC group and EAC group, respectively.

A) USC group. B) EAC group. In clustering dendrogram, blue stands for good prognosis samples while yellow stands for poor prognosis samples. Red means up-regulated while green means down regulated.

Figure 3. Venn diagrams show little overlap for DEGs derived from the USC and EAC groups, respectively.

Left) DEGs from comparing late stage versus early stage in the USC group and EAC group, respectively. Right) DEGs from comparing good prognosis versus poor prognosis in the USC group and EAC group, respectively. A) DEGs as defined by P-value<0.01. B) DEGs with at least 1.5-fold change. C) DEGs with at least 2-fold change.

Figure 4. Venn diagrams show no overlap between stage-related DEGs (late versus early) and outcome-related DEGs (good versus poor) in both USC and EAC groups.

EvL means DEGs from comparing late stage versus early stage patients. GvB means DEGs from comparing good prognosis versus poor prognosis patients. A) DEGs as defined by P-value<0.01 in USC group. B) DEGs as defined by P-value<0.01 in EAC group.

Figure 5. Enriched function annotation of differentially expressed genes (P<0.01) identified by microarray.

Enriched functional annotations are reported by NCBI DAVID API server with default setting. The number following each enriched functional term is the number of annotated DEGs. A) Enriched functional annotation for stage-related DEGs (late versus early) in USC group. B) Enriched functional annotation for stage-related DEGs in EAC group. C) Enriched functional annotation for outcome-related DEGs (good versus poor) in USC group. D) Enriched functional annotation for outcome-related DEGs in EAC group.

Figure 6. qRT-PCR validation of differentially expressed genes (P<0.01) with at least two-fold expression change as identified by microarray.

A) stage-related DEGs (late versus early) in USC group. B) stage-related DEGs in EAC group. C) Outcome-related DEGs (good versus poor) in USC group. D) Outcome-related DEGs in EAC group. Blue bar is the fold change estimated by qRT-PCR, while red bar is the fold change estimated by microarray. The fold change is shown in log2 scale (i.e., >1 means at least 2-fold up, while <−1 means at least 2-fold down). The three genes with less than two-fold change in expression level based on qRT-PCR are FST, LMO4 and RPRM.