Identification of estrogen responsive genes using esophageal squamous cell carcinoma (ESCC) as a model

Abstract

Background: Estrogen therapy has positively impact the treatment of several cancers, such as prostate, lung and breast cancers. Moreover, several groups have reported the importance of estrogen induced gene regulation in esophageal cancer (EC). This suggests that there could be a potential for estrogen therapy for EC. The efficient design of estrogen therapies requires as complete as possible list of genes responsive to estrogen. Our study develops a systems biology methodology using esophageal squamous cell carcinoma (ESCC) as a model to identify estrogen responsive genes. These genes, on the other hand, could be affected by estrogen therapy in ESCC.

Results: Based on different sources of information we identified 418 genes implicated in ESCC. Putative estrogen responsive elements (EREs) mapped to the promoter region of the ESCC genes were used to initially identify candidate estrogen responsive genes. EREs mapped to the promoter sequence of 30.62% (128/418) of ESCC genes of which 43.75% (56/128) are known to be estrogen responsive, while 56.25% (72/128) are new candidate estrogen responsive genes. EREs did not map to 290 ESCC genes. Of these 290 genes, 50.34% (146/290) are known to be estrogen responsive. By analyzing transcription factor binding sites (TFBSs) in the promoters of the 202 (56+146) known estrogen responsive ESCC genes under study, we found that their regulatory potential may be characterized by 44 significantly over-represented co-localized TFBSs (cTFBSs). We were able to map these cTFBSs to promoters of 32 of the 72 new candidate estrogen responsive ESCC genes, thereby increasing confidence that these 32 ESCC genes are responsive to estrogen since their promoters contain both: a/mapped EREs, and b/at least four cTFBSs characteristic of ESCC genes that are responsive to estrogen. Recent publications confirm that 47% (15/32) of these 32 predicted genes are indeed responsive to estrogen.

Conclusion: To the best of our knowledge our study is the first to use a cancer disease model as the framework to identify hormone responsive genes. Although we used ESCC as the disease model and estrogen as the hormone, the methodology can be extended analogously to other diseases as the model and other hormones. We believe that our results provide useful information for those interested in genes responsive to hormones and in the design of hormone-based therapies.

Figure 1

Defining the minimum number of cTFBSs required for the identification of estrogen responsive ESCC genes. This figure is a graphical representation of the proportion of genes that contain multiple cTFBSs mapped to their promoters. The graph depicts the threshold defining the maximum difference between the known estrogen responsive genes (C1 and C3) relative to the background set (C4).

Figure 2

An overview of the cTFBSs and their regulatory effects on the ESCC genes. The figure represents a heat map of cTFBSs that are significantly over-represented in the promoters of the known estrogen response genes in ESCC (columns) mapped to the promoters of the new candidate estrogen response genes in C2A (rows). The red shading depicts the association between the gene promoter and the cTFBSs, while white depicts no association.

Figure 3

An illustration of the ERs transcriptional activation process. This figure is a pictorial representation of the known “estrogen → ER → ERE” dependent transcriptional activation process that requires the candidate estrogen responsive gene products, AKAP13 and CDC25B, as co-factors.