Integrated analysis of dysregulated lncRNA expression in breast cancer cell identified by RNA-seq study

Abstract

Among all the sequencing techniques, RNA sequencing (RNA-seq) has galloped with pace adopting the profiling of transcriptomic data in almost every biological analytics area like gene regulation study, development biology and clinical research. Recently the discovery of differentially expressed genes across different conditions has outshone the barrier of genetic & epigenetic regulations. The present work identified and analyzed differentially expressed novel long non-coding RNAs (lncRNAs) for breast cancer. A complex computational pipeline was adopted for the study which includes analysis of 18498 differentially expressed genes with 4114 up-regulated and 3475 down-regulated transcripts. The overexpression of lnc-MTAP (CDKN2B-AS1), lnc-PCP4 (DSCAM-S1), and lnc-FAM (H19) in breast cells suggests that these lncRNAs may have significant role to play in breast cancer. These results validated the relevance of the dysregulation pattern in cancer cells due to the presence of lncRNAs. The study further opens a new scope for experimental analysis to confirm the aberrant expression pattern of these lncRNAs which may act as potential bio-markers for the diagnosis and early detection of breast cancer.

Long non‐coding RNA SOX21‐AS1 enhances the stemness of breast cancer cells via the Hippo pathway

“…Meanwhile, the function and mechanism of lncRNA in the development and prognosis of breast cancer have been increasingly emphasized [27]. Therefore, the in‐depth exploration of lncRNA has a very important role in the early diagnosis of breast cancer, including the search for potential biomarkers and the prognosis [28]. In the present study, we investigated lncRNA SOX21‐AS1 and found that the expression of SOX21‐AS1 in breast cancer was disordered.…”

Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells

“…CDKN2B-AS1 (ANRIL) is located in the 9q21.3 region with rs62560775, associated with lung adenocarcinoma and BC susceptibility [ 203 ]. CDKN2B-AS1 is upregulated in MCF10A breast epithelial cells [ 204 ] and in breast tumors [ 205 ]. CDKN2B-AS1 was identified as a member of the ceRNA network for MMP1/MMP11-miR-145-5p and speculated to be involved in the development of early BC [ 205 ].…”

Unraveling long non-coding RNAs through analysis of high-throughput RNA-sequencing data

“…Tripathi et al. in their paper thoroughly described the integrated analysis of dysregulated lncRNAs, lnc-PCP4, and lnc-FAM in breast cancer expression using RNA-seq study [69] . In a parallel study done by a group of researchers from Scripps Research Institute, RNA seq data was analyzed to demonstrate region specific enrichment of populations of lncRNAs and mRNAs in the mouse hippocampus and pre-frontal cortex (PFC) which were found to be involved in memory storage and neuropsychiatric disorders [70] .…”