Identification of differentially expressed lncRNAs and mRNAs in luminal-B breast cancer by RNA-sequencing

Abstract

Background: Luminal B cancers show much worse outcomes compared to luminal A. This present study aims to screen key lncRNAs and mRNAs correlated with luminal-B breast cancer. Methods: Luminal-B breast cancer tissue samples and adjacent tissue samples were obtained from 4 patients with luminal-B breast cancer. To obtain differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) between luminal-B breast cancer tumor tissues and adjacent tissues, RNA-sequencing and bioinformatics analysis were performed. Functional annotation of DEmRNAs and protein-protein interaction networks (PPI) construction were performed. DEmRNAs transcribed within a 100 kb window up-or downstream of DElncRNAs were searched, which were defined as cis nearby-targeted DEmRNAs of DElncRNAs. DElncRNA-DEmRNA co-expression networks were performed. The mRNA and lncRNA expression profiles were downloaded from The Cancer Genome Atlas (TCGA) database to validate the expression patterns of selected DEmRNAs and DElncRNAs. Results: A total of 1178 DEmRNAs and 273 DElncRNAs between luminal-B breast cancer tumor tissues and adjacent tissues were obtained. Hematopoietic cell lineage, Cytokine-cytokine receptor interaction, Cell adhesion molecules (CAMs) and Primary immunodeficiency were significantly enriched KEGG pathways in luminal-B breast cancer. FN1, EGFR, JAK3, TUBB3 and PTPRC were five hub proteins of the PPI networks. A total of 99 DElncRNAs-nearby-targeted DEmRNA pairs and 1878 DElncRNA-DEmRNA co-expression pairs were obtained. Gene expression results validated in TCGA database were consistent with our RNA-sequencing results, generally. Conclusion: This study determined key genes and lncRNAs involved in luminal-B breast cancer, which expected to present a new avenue for the diagnosis and treatment of luminal-B breast cancer.

Long Non-Coding RNA PCED1B-AS1 Promotes the Progression of Clear Cell Renal Cell Carcinoma Through miR-484/ZEB1 Axis

“…It is reported that lncRNA PCED1B-AS1 is up-regulated in luminal B breast cancer and glioblastoma tissues; PCED1B-AS1 can bind to the 5ʹ-UTR of HIF-1α mRNA and facilitates HIF-1α translation, thereby promoting the Warburg effect and tumorigenesis of glioblastoma. 22,23 In addition, PCED1B-AS1 can modulate the miR-194-5p/PCED1B axis to promote glioma cell proliferation and inhibit apoptosis. 24 In the current research, for the first time, we investigated the expression and biological function of PCED1B-AS1 in ccRCC.…”

The circulating level of Non-coding RNA for breast cancer diagnosis

“…Furthermore, we used meta-regression to analysis the source of samples which divided into blood (8 studies), plasma (13 studies), and serum (11 studies) three groups. The p-value of these three groups (p=0.4670 in blood group; p=0.5495 in plasma group; p=0.3517 in serum group) were more than 0.05, which means the sample source is not the reason for the formation of heterogeneity (supplement table [3][4][5]. We also test meta-analysis of the SEN, SPE, and AUC for these three groups (blood, plasma, and serum), the pooled SEN values were 0.84, 0.82, and 0.79, SPE values were 0.84, 0.84, and 0.80, and AUC values were 0.91, 0.90, and 0.85, respectively (supplement Figure 3), showing little change in analysis.…”

“…has been associated with various cancers [5]. The non-coding RNA (ncRNA) is a function of RNA molecular that is transcribed from DNA but no or limited protein-coding potential.…”

Long non‑coding RNA PCED1B‑AS1 promotes pancreatic ductal adenocarcinoma progression by regulating the miR‑411‑3p/HIF‑1α axis

“…In non-small lung cancer, knockdown of lncRNA colon cancer associated transcript 1 suppressed cancer cell proliferation and sensitized cancer cells to gefitinib (11). lncRNA PC-esterase domain containing 1B antisense RNA 1 (PCED1B-AS1) was found to be involved in the regulation of macrophage apoptosis and autophagy in active tuberculosis (12,13); additionally, it has been demonstrated that PCED1B-AS1 is abnormally expressed in gliomas and breast cancer tissues, where it functions as an oncogenic lncRNA (14,15). However, its biological function, mechanistic partners and clinical value in PDAC have not been assessed.…”