Bioinformatic Identification of a Breast Tissue-Specific Gene Expression Profile

Abstract

The clinical significance of cancer biomarkers is undoubtedly, especially for those with tissue specificity. To date, there are not any widely-accepted breast tissue-specific biomarkers. The revolutionized development of gene analysis techniques has generated a vast amount of data on human transcriptomics and proteomics, allowing us to search for breast tissue-specific biomarkers in a systematic way. In this study, by integrating and investigating the standardized raw RNA-Seq data of near 50,000 human genes across 88 human tissues from the GTEx, the Illumina Body Map, and the RIKEN FANTOM5 project, we identified that only 96 genes in human genome were potential breast tissue-specific biomarkers, with the majority of these genes were poorly understood at the current stage. Moreover, by further analyzing the TCGA project, the GEPIA database, the Ensemble Genome Browser, and the Kaplan-Meier Plotter database, we demonstrated that two breast-specific genes, ANKRD30A and LINC00993 that we previously identified to be considerably down-regulated in TNBC, may play important roles in breast cancer because of their breast cancer specificity, distinct expression patterns in breast cancer subtypes, and effectiveness for prognostic predictions. In summary, we present a potential breast tissue-specific gene expression profile, an updated strategy for the search of tissue-specific biomarkers, and reasons for performing further researches on these promising biomarkers in breast cancer. Funding Statement: This study is supported by the China Scholarship Council (CSC). Declaration of Interests: The authors have declared no conflicts of interest related to the present manuscript. Ethics Approval Statement: Not required.