Microarray expression profiling of dysregulated long non-coding RNAs in triple-negative breast cancer

Abstract

Triple-negative breast cancer (TNBC) represents a collection of malignant breast tumors that are often aggressive and have an increased risk of metastasis and relapse. Long non-coding RNAs are generally defined as RNA transcripts measuring 200 nucleotides or longer that do not encode for any protein. During the past decade, increasing evidence has shown that lncRNAs play important roles in oncogenesis and tumor suppression; however, the roles of lncRNAs in TNBC are poorly understood. To address this issue, we used Agilent human lncRNA microarray chips and bioinformatics tools, including Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), to assess lncRNA expression in 3 pairs of TNBC tissues. A dysregulated lncRNA expression profile was identified by microarray and verified by qRT-PCR in 48 pairs of breast cancer subtype tissues. Metastasis is the major cause of cancer-related deaths, including those in TNBC, and the presence of dormant residual disseminated tumor cells (DTC) may be a key factor leading to metastasis. ANKRD30A, a potential target for breast cancer immunotherapy, is currently one of the most used DTC markers. Notably, we found the expression levels of the novel intergenic lncRNA LINC00993 to be associated with the expression levels of ANKRD30A. Furthermore, our qRT-PCR data indicated that the expression of LINC00993 was also associated with the expression of the estrogen receptor. In conclusion, our study identified a set of lncRNAs that were consistently aberrantly expressed in TNBC, and these dysregulated lncRNAs may be involved in the development and/or progression of TNBC.

Comprehensive Analysis of Differentially Expressed Profiles of lncRNAs/mRNAs and miRNAs with Associated ceRNA Networks in Triple-Negative Breast Cancer

“…KEGG pathway analysis displayed that 7 cancer-related pathways were significantly enriched in metabolic pathways, PI3K-Akt signaling pathway, pathway in cancer, transcriptional misregulation in cancer, cell cycle, proteoglycans in cancer and PPAR signaling pathway, suggesting these mRNAs could play the crucial roles in the tumorigenesis and development of TNBC. Our data support Chen et al's finding [38]. Subsequently, the prognostic significance of these differentially expressed mRNAs was also Cellular Physiology and Biochemistry Cellular Physiology and Biochemistry explored.…”

Functions and Roles of Long-Non-Coding RNAs in Human Nasopharyngeal Carcinoma

“…Accumulating evidence indicate that lncRNAs, by interacting with DNA, RNA, protein molecules and/or their combinations, play a critical role in regulation of cellular processes including genetic imprinting, chromatin remodeling, splicing regulation, mRNA decay, transcription, and translational regulation [33-36]. Expression and activity of lncRNAs are deregulated in several types of human cancer, therefore, aberrant expressions of lncRNAs can cause various human diseases, including cancers [34, 37] and contribute to tumor occurrence and development through numerous mechanisms, ranging from epigenetic, transcriptional and posttranscriptional regulation of relevant genes to the control of cell cycle distribution, cell differentiation, and epigenetic modifications [38-41]. Nevertheless, the functions and mechanisms of the vast majority of lncRNAs still remain unknown.…”

Identification of aberrantly methylated differentially expressed genes in breast cancer by integrated bioinformatics analysis

“…Microarrays can quickly and accurately detect gene expression in tumor tissues and normal tissues on a large scale, while bioinformatics can efficiently analyze differential genes as well as screen core genes . Studies on gene expression have been carried out to identify differentially expressed genes (DEGs) in breast cancer . Furthermore, methylation microarray profiling has been applied to identify differentially methylated genes (DMGs) between breast tumor specimens and normal specimens .…”