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Bioinformatic Identification of a Breast‐Specific Transcript Profile
Author(s) -
Chen Chen,
Yang Liwen,
Rivandi Mahdi,
Franken André,
Fehm Tanja,
Neubauer Hans
Publication year - 2020
Publication title -
proteomics – clinical applications
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.948
H-Index - 54
eISSN - 1862-8354
pISSN - 1862-8346
DOI - 10.1002/prca.202000007
Subject(s) - breast cancer , clinical significance , ankyrin repeat , biology , gene expression profiling , cancer , gene , computational biology , oncology , gene expression , cancer research , bioinformatics , medicine , genetics
Purpose To identify a breast‐specific transcript profile for the first time, and present an updated bioinformatics strategy for searching tissue‐specific transcripts and predicting their significance in cancer. Experimental Design The RNA‐seq data of 49 311 transcripts in 88 human tissues from the GTEx, the Illumina Body Map, and the RIKEN FANTOM5 project are integrated to screen breast‐specific transcripts. Gene Expression Profiling Interactive Analysis, TGCA, and Kaplan–Meier Plotter are used to examine their expression in cancer tissues and values for prognosis prediction. Results Only 96 transcripts in human genome are breast‐specific for women. Among them, ankyrin repeat domain 30A (ANKRD30A) and long intergenic non‐protein coding RNA 993 (LINC00993) are further analyzed. The two transcripts are also breast‐specific in 33 types of common female cancer and are often dysregulated in breast cancer tissues. Their expression is higher in the luminal breast cancer while significantly downregulated in triple‐negative breast cancer. Moreover, the high expression levels of ANKRD30A and LINC0993 in breast cancer tissues indicate a better prognosis of patients with breast cancer. Conclusions and Clinical Relevance Breast‐specific transcripts in human genome are rare and poorly understood currently. The data indicate that these breast‐specific biomarkers are promising candidates for screening early cancer, assessing treatment response, monitoring recurrence, identifying metastatic tumor origin, and serving as potential targets for immunotherapy.