Bioinformatic identification of a breast-specific transcript profile

Markers with tissue specificity are important for early cancer detection, aiding postoperative surveillance, monitoring treatment response, and delivery of targeted drugs. The values of traditional markers for the early screening and recurrence monitoring of breast cancer are limited because of unsatisfactory sensitivity or tissue specificity, thus a comprehensive view of breast-specific markers is needed to find novel candidates with potential clinical values. High-throughput gene analysis techniques have generated a vast amount of data on human transcriptomics, enabling the search of breast-specific biomarkers systematically. By analyzing the normalized RNA-Seq data of 88 human tissues from the GTEx, the Illumina Body Map, and the RIKEN FANTOM5 project, we identified that only 96 transcripts in human genome were breast-specific, including 19 protein-coding genes and 77 non-coding RNAs. Two breast-specific transcripts of interest, ANKRD30A and LINC00993, were further analyzed. Based on data from the GEPIA database, the expression of ANKRD30A and LINC00993 were breast-cancer-specific in 33 types of cancer tissues in adult women. Moreover, the two transcripts were often dysregulated in breast cancer tissues, and their expression was higher in the luminal subtype of breast cancer while significantly down-regulated in triple-negative breast cancer. The high expression levels of ANKRD30A and LINC0993 in breast cancer tissues were correlated with a better breast cancer prognosis. In conclusion, we present an updated bioinformatics strategy for the search of breast-specific transcripts as well as approaches to predict their significance for breast cancer, including breast cancer specificity, expression correlation with clinical features of cancer, and roles for prognostic prediction.

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Publication History

Article published online:
01 June 2021