The feasibility of using biopsy samples from esophageal cancer for comprehensive gene expression profiling

Advanced esophageal cancer has been recently treated by multimodal therapy including preoperative chemotherapy or chemoradiotherapy and surgery. A biopsy sample provides a valuable specimen for understanding the biological characteristics of individual esophageal cancer. Pretreatment prediction of the response to chemotherapy or radiotherapy based on biological characteristics using biopsy samples is a desirable goal. In using biopsy samples for molecular analysis, there are two problems; the proportion of cancer cells and the intratumor heterogeneity. This study was conducted to investigate the feasibility of using endoscopic biopsy samples of esophageal squamous cell cancer (ESCC) for comprehensive gene expression profiling (GEP). Comprehensive GEP was performed in 40 bulky ESCC specimens and 10 normal esophageal epithelial specimens from patients who underwent esophageal resection and 52 endoscopic ESCC biopsy samples from 26 patients (two samples per one patient). Unsupervised hierarchical cluster analysis showed distinct profiles between the bulky ESCC specimens and normal epithelial specimens. Also, unsupervised hierarchical cluster analysis revealed distinct profiles between the biopsy ESCC samples and normal epithelial specimens. Moreover, a couple of biopsy samples taken from different locations of the same tumor were closely clustered together. That is, biopsy ESCC samples were distinguished from normal esophageal epithelial specimens and the intratumor heterogeneity of GEP was smaller than intertumor heterogeneity. GEP using biopsy ESCC samples is feasible and has the potential to represent the biological properties.