New insight into long non-coding RNAs associated with bone metastasis of breast cancer based on an integrated analysis

Abstract

Background Bone is the most common site of metastatic breast cancer, and it is a leading cause of breast cancer-related death. This study aimed to explore bone metastasis-related long non-coding RNAs (lncRNAs) in breast cancer. Methods Four mRNA datasets and two lncRNA datasets of bone metastasis, lung metastasis and liver metastasis of breast cancer were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) in group of bone metastasis vs lung metastasis and bone metastasis vs liver metastasis, as well as the overlap of the two groups, were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and protein–protein interaction (PPI) network construction of DEmRNAs were conducted. The cis nearby-targeted DEmRNAs of DElncRNAs were obtained. Quantitative real-time polymerase chain reactions (qRT-PCR) was used to detect the expression levels of selected DEmRNAs and DElncRNAs. LOC641518-lymphoid enhancer-binding factor 1 (LEF1) pair was selected to verify its role in migration and invasion capability of breast cancer cells by wounding healing assay and transwell invasion assay. Results A total of 237 DEmRNAs were obtained in bone metastasis compared with both lung metastasis and liver metastasis. A total of three DElncRNAs in bone metastasis compared with both lung metastasis and liver metastasis were obtained. A total of seven DElncRNA-nearby-targeted DEmRNA pairs and 15 DElncRNA-nearby-targeted DEmRNA pairs in group of bone metastasis vs lung metastasis and bone metastasis vs liver metastasis, were detected, respectively. Four cis LncRNA-mRNA interaction pairs were identified, which are LOC641518-LEF1, FLJ35024-Very Low Density Lipoprotein Receptor (VLDLR), LOC285972-Retinoic Acid Receptor Responder 2 (RARRES2) and LOC254896-TNF receptor superfamily member 10c (TNFRSF10C). qRT-PCR using clinical samples from our hospital confirms the bioinformatics prediction. siRNA knocking down LOC641518 down-regulates LEF1 mRNA expression, and reduces the migration and invasion capability of breast cancer cells. Conclusions We concluded that four LncRNA-mRNA pairs, including LOC641518-LEF1, may play a central role in breast cancer bone metastasis.

Long noncoding RNA CCDC183-AS1 depletion represses breast cancer cell proliferation, colony formation, and motility by sponging microRNA-3918

“…Tumor metastasis and unlimited growth manifest challenges to the therapy and clinical efficiency of BC [20]. LncRNAs are deregulated in BC and contribute to the regulation of complex cellular behaviors [21][22][23]. Accordingly, studying the upstream regulatory mechanisms underlying BC growth and metastasis will be favorable for the development of To date, accumulated studies have illustrated the significance of lncRNAs in the genesis and promotion of BC.…”

Plasminogen activator, urokinase enhances the migration, invasion, and proliferation of colorectal cancer cells by activating the Src/ERK pathway

“…Transwell migration and invasion assays were performed according to the previous publication ( 17 ). For the invasion assay, Matrigel (Solarbio) was pre-coated in the upper Transwell chamber, and the SW480 and SW620 cells were inoculated into the upper Transwell chamber (BD, CA, USA) (approximately 1×10 5 /well) with 200 µL of serum-free medium.…”

Identification of lncRNA-mRNA interactions and genome-wide lncRNA annotation in animal transcriptome profiling

“…lncRNA has well-known tissue-specific, species-specific, and conditional-specific tendencies. Even the same individual can express lncRNA differently depending on what kind of tissue it is, and even the same tissue can express differently depending on the species (96,(106)(107)(108)(109)(110). Moreso, the tissue-specific characteristics of lncRNA demonstrated higher results even when compared to mRNA through the tissue specificity index calculated numerically in mammals (96,111).…”