Analysis of normal tissues adjacent to the tumour-specific expressed genes in breast cancer

Abstract

Normal tissues adjacent to the tumour (NAT) are widely used as controls in comparative studies to search for cancer-associated genes. However, the gene expression profiles between NAT and non-tumour-bearing tissues are different. The presence of NAT-specific expressed genes often hinders traditional transcriptional profiles studies. Further, studies on the differences in gene expression profiles between NAT and tumour-free tissues are infrequently performed. In this study, we sequenced and analysed the transcriptomes of tumour tissues (T), matched NAT and contralateral breast normal tissues (CBN) of 14 breast cancer patients, and identified 102 differentially expressed genes (DEGs) between CBN and NAT. Gene enrichment and protein-protein interaction (PPI) analyses revealed that these DEGs are significantly enriched in TNF (tumour necrosis factor) signalling and EMT (epithelial-mesenchymal transition) gene sets closely associated with oncogenesis. Comparative analyses of the transcriptomic profiles between NAT and CBN, NAT and T identified 23 NAT-specific highly-expressed genes, namely tumour-adjacent speci?cally activated (TASA) genes. These genes were significantly enriched in TNF signalling gene set, and 15 of which have not been previously reported. The results indicate that TASA genes are common in adjacent tissues and are related to the TNF signalling in the immune system. The tumour-adjacent tissues harbour tumour-like expressed genes that could contribute to tumour initiation but are often missed in NAT-T pair-wise studies.