Long intergenic non-coding RNA expression signature in human breast cancer

Abstract

Breast cancer is a complex disease, characterized by gene deregulation. There is less systematic investigation of the capacity of long intergenic non-coding RNAs (lincRNAs) as biomarkers associated with breast cancer pathogenesis or several clinicopathological variables including receptor status and patient survival. We designed a two-stage study, including 1,000 breast tumor RNA-seq data from The Cancer Genome Atlas (TCGA) as the discovery stage, and RNA-seq data of matched tumor and adjacent normal tissue from 50 breast cancer patients as well as 23 normal breast tissue from healthy women as the replication stage. We identified 83 lincRNAs showing the significant expression changes in breast tumors with a false discovery rate (FDR) < 1% in the discovery dataset. Thirty-seven out of the 83 were validated in the replication dataset. Integrative genomic analyses suggested that the aberrant expression of these 37 lincRNAs was probably related with the expression alteration of several transcription factors (TFs). We observed a differential co-expression pattern between lincRNAs and their neighboring genes. We found that the expression levels of one lincRNA (RP5-1198O20 with Ensembl ID ENSG00000230615) were associated with breast cancer survival with P < 0.05. Our study identifies a set of aberrantly expressed lincRNAs in breast cancer.

Peer Review #2 of "Long non-coding RNA, LINC01614 as a potential biomarker for prognostic prediction in breast cancer (v0.1)"

“…These three lncRNAs-based signature could facilitate the prognosis prediction of esophageal squamous cell carcinoma. Moreover, Zhang et al also found that LINC01614 was highly expression in ER positive BRCA which was in line with our result (Zhang et al 2016b). These findings highlighted the potential role of LINC01614 in BRCA and it might be an useful biomarker for BRCA prognostic prediction.…”

Transcriptome sequencing to detect the potential role of long non-coding RNAs in bovine mammary gland during the dry and lactation period

“…Increasing data had shown that lncRNAs could regulate gene expression both at transcriptional and post-transcriptional levels, including the regulation of splicing, mRNA processing, and translation [ 55 ]. It had been demonstrated that some lncRNAs implicated in breast normal development and cancer based on their expression pattern, function and localization in human and mouse [ 56 , 57 ]. However, limited researches had been reported the regulation mechanism of lncRNAs on bovine lactation.…”

Upregulation of Long Non-Coding RNA DRAIC Correlates with Adverse Features of Breast Cancer

“…In breast cancer, DRAIC expression was identified as a potential onco-lncRNA based on its elevated expression in tumor tissues compared to the adjacent normal tissues [23]. It was shown to be higher in ER positive breast cancer patients from 4 different studies [23,24,25,26].…”